The functional guts of the Kleisli query system

Kleisli is a modern data integration system that has made a significant impact on bioinformatics data integration. The primary query language provided by Kleisli is called CPL, which is a functional query language whose surface syntax is based on the comprehension syntax. Kleisli is itself implemented using the functional language SML. This paper describes the influence of functional programming research that benefits the Kleisli system, especially the less obvious ones at the implementation level.

[1]  Limsoon Wong,et al.  An introduction to Remy's fast polymorphic record projection , 1995, SGMD.

[2]  Peter Buneman,et al.  Structural Recursion as a Query Language , 1992, DBPL.

[3]  Limsoon Wong,et al.  Kleisli, a functional query system , 2000, J. Funct. Program..

[4]  Nick Roussopoulos,et al.  Interoperability of multiple autonomous databases , 1990, CSUR.

[5]  Jeffrey D. Ullman,et al.  Principles of Database and Knowledge-Base Systems, Volume II , 1988, Principles of computer science series.

[6]  S F Altschul,et al.  Local alignment statistics. , 1996, Methods in enzymology.

[7]  Limsoon Wong,et al.  BioKleisli: a digital library for biomedical researchers , 1997, International Journal on Digital Libraries.

[8]  David Jordan,et al.  The Object Database Standard: ODMG 2.0 , 1997 .

[9]  Carole A. Goble,et al.  TAMBIS: Transparent Access to Multiple Bioinformatics Information Sources , 1998, ISMB.

[10]  Peter Buneman,et al.  Database programming in Machiavelli—a polymorphic language with static type inference , 1989, SIGMOD '89.

[11]  Dan Suciu,et al.  On Two Forms of Structural Recursion , 1995, ICDT.

[12]  Limsoon Wong,et al.  FIMM, a database of functional molecular immunology , 2000, Nucleic Acids Res..

[13]  Limsoon Wong,et al.  A protein patent query system powered by Kleisli , 1998, SIGMOD '98.

[14]  E. F. Codd,et al.  A relational model of data for large shared data banks , 1970, CACM.

[15]  R. G. G. Cattell,et al.  The Object Database Standard: ODMG-93 , 1993 .

[16]  J. Michael Spivey,et al.  A Functional Theory of Exceptions , 1990, Sci. Comput. Program..

[17]  Limsoon Wong,et al.  Querying Nested Collections , 1994 .

[18]  Didier Rémy,et al.  Type checking records and variants in a natural extension of ML , 1989, POPL '89.

[19]  N W Matheson,et al.  The GDB Human Genome Data Base Anno 1992. , 1992, Nucleic acids research.

[20]  E. F. Codd,et al.  A Relational Model for Large Shared Data Banks , 1970 .

[21]  Philip Wadler,et al.  Comprehending monads , 1990, LISP and Functional Programming.

[22]  S Walsh,et al.  ACEDB: a database for genome information. , 1998, Methods of biochemical analysis.

[23]  J. Davenport.  Editor , 1960 .

[24]  Lawrence C. Paulson,et al.  A Higher-Order Implementation of Rewriting , 1983, Sci. Comput. Program..

[25]  G. Schuler,et al.  Entrez: molecular biology database and retrieval system. , 1996, Methods in enzymology.

[26]  Jennifer Widom,et al.  Object exchange across heterogeneous information sources , 1995, Proceedings of the Eleventh International Conference on Data Engineering.

[27]  Chen,et al.  Using Kleisli to Bring Out Features in BLASTP Results. , 1998, Genome informatics. Workshop on Genome Informatics.

[28]  Val Tannen,et al.  Logical and Computational Aspects of Programming with Sets/Bags/Lists , 1991, ICALP.

[29]  Dan Suciu,et al.  Bounded Fixpoints for Complex Objects , 1993, Theor. Comput. Sci..

[30]  Limsoon Wong,et al.  Local properties of query languages , 1997, Theor. Comput. Sci..

[31]  D Benton,et al.  Bioinformatics--principles and potential of a new multidisciplinary tool. , 1996, Trends in biotechnology.

[32]  Limsoon Wong,et al.  Principles of Programming with Complex Objects and Collection Types , 1995, Theor. Comput. Sci..

[33]  P G Baker,et al.  Recent developments in biological sequence databases. , 1998, Current opinion in biotechnology.

[34]  Limsoon Wong,et al.  Query Languages for Bags and Aggregate Functions , 1997, J. Comput. Syst. Sci..

[35]  K. H. Fasman,et al.  The GDB Human Genome Data Base anno 1994. , 1994, Nucleic acids research.

[36]  Shahrokh Saeednia,et al.  How to maintain both privacy and authentication in digital libraries , 2000 .